Once Upon a Time Machine 2-9: Aliens of New New York
by Doctor's Torchwood
Summary: The search for a magical artifact leads the Doctor and Clara five billion years in the future in New New York, where they are surprised to find the heroes of Storybrooke. The hunt for the magic brings danger in the city and unleashes dark power. Can they all make it back to Storybrooke in one piece?
1. The Flying Pirate Ship

_I do not own Doctor Who or Once Upon a Time. Only this story. Enjoy!_

* * *

Chapter 1: The Flying Pirate Ship

"Do you still think about him?" Danny Pink asked Clara Oswald as they walked down the hallway of her apartment building together. Danny and Clara just had a pleasant night out to dinner. Danny's question was referring to the Doctor. Clara promised Danny that she stopped traveling with the Doctor, even though this was a lie.

"Sometimes." Clara said as they came to the door to Clara's apartment. "I'm still happy being here on Earth with you."

The couple then shared a goodnight kiss before Clara entered her apartment alone and closed the door behind her. She had a truly wonderful date with Danny. However, Clara's night was far from over. As she walked into the living room and put her purse down on the table, she saw the TARDIS, sitting right in front of the window. Soon, the Doctor stepped out of the TARDIS doors.

"Oh good. You're home." The old Time Lord said. "I found it."

"Found what?" Clara asked.

"The last Eye." He said.

The Doctor was referring to the three Eyes of the Mystic Fates. These were three glass eyeballs. Each eye contained massive amounts of magical power and they were scattered across time and space. The Eye of Life was in Regina's vault in Storybrooke. She acquired it when she was the Evil Queen. The Dark Curse brought it to Storybrooke along with her other magical possessions. The Eye of Death was inside the TARDIS after Clara stole it from Peter Pan back in Neverland. The Eye of Birth was in Oz, but it was sent to an unknown world in the future to keep the Wicked Witch from ever getting her hands on it again. The Doctor was determined to find the Eye of Birth so that no one else could. Not for selfish reasons of course. The Doctor just wanted to be sure that the Daleks, the Cybermen, the Sontarans, or any of his other foes didn't find it.

"Where is it?" Clara asked.

"It's on another a planet. It's a world I've been to a few times before. I went with Rose and Martha." The Doctor said.

Clara remembered Rose and Martha fondly. She hadn't seen them since they fought Peter Pan and the Daleks on Neverland together. Then, Rose went back to her parallel world and Martha went back with Mickey to help fight aliens on Earth with Torchwood.

"Which world?" Clara asked.

"It's called New Earth." The Doctor replied. "Five billion years in the future, the Earth dies and humanity finds a new one. The Eye is somewhere in its largest city."

"Which is?" Clara asked.

"New New York." The Doctor said.

"New New York?" Clara asked.

"Technically it's the fifteenth New York since the original, but it's easier just to say New New York." The Doctor said. "What are you waiting for. Get inside."

"Doctor." Clara said. "I'm tired. I've just had a wonderful night with Danny."

"Getting the Eye is more important than your boyfriend." The Doctor said. "Besides. New New York is special. It's one of the worlds where magic is possible. That means you can use your powers there."

Clara rarely went to a world where magic was possible. The only places she'd been where she could use her powers were the Enchanted Forest, Agrabah, Wonderland, Neverland, Arendelle, and Oz. She did want the opportunity to use magic again.

"You hate magic though." Clara said.

"I'm looking for magic." The Doctor said. "You could use magic to help me find it. Please just get in. The longer we stay here, the longer this will take."

Clara knew it was no use arguing with him on this one. So, wearing a red dress and black heals, Clara boarded the TARDIS for another adventure.

* * *

New New York, New Earth

The TARDIS materialized in a field across the harbor from the city. The Doctor and Clara stepped outside and saw a beautiful city in the distance. There were skyscrapers taller than any on modern day Earth and flying cars zoomed across the sky.

"It's amazing." Clara said.

"It's huge." The Doctor said. "Thats why I need your magic to help find it."

Clara took the Doctor's hint and extended her arms. She was preparing to cast some kind of location spell. However, something strange distracted her. There were cars flying through the air, but there was something else in the sky above. It was more unusual than anything else. In the distance, Clara and the Doctor saw an old pirate ship flying in the air. The main sail on this ship was not white. It was black. A pirate ship with a black sail was flying through the air, and coming towards the Doctor and Clara. The ship flew lower and lower. It was clearly trying to land in the harbor. The two time travelers instinctively ran closer to the water to see what this ship was doing here. The ship made a large splash as it hit the water and sailed closer to the shore. As it moved closer now in the water, the Doctor and Clara realized that they recognized this ship. It was the Jolly Roger, Captain Hook's ship. The Doctor and Clara soon recognized some of the people on the ship as well. They could make out the faces of Hook, Emma Swan, Regina, Henry, Mary Margaret, David, Mr. Gold, Neal, and Tinker Bell. There were some other people that they didn't recognize as well. The ship soon reached the shore and parked there. Upon seeing the Doctor and Clara, the Storybrooke heroes used magic to transport themselves to the ground.

"What are you all doing here?" The Doctor asked. "How did you even get here?"

"That depends on where here is." Emma said. "What is this place?"

"You didn't mean to come here?" Clara asked.

"We meant to go back to Storybrooke." Regina said.

"Back to Storybrooke?" The Doctor asked. "Where were you all before?"

"Neverland." Hook said. "Pan kidnapped Henry. He's the one with the heart of the truest believer. We got him back and left Pan there to die."

"Regina trapped Pan's Shadow on the sail to take us home." Mary Margaret said.

"So where did it take us instead?" David asked.

"You're on another world." The Doctor said.

"In the future." Clara added.

"How could we have time traveled?" Neal asked.

"Perhaps Pan's Shadow is more powerful than we thought." Gold said.

"You're five billion years in the future." The Doctor said.

"How many?" Emma asked, sounding very surprised.

"Five billion." Clara said. "We're here looking for the Eye of Birth."

"It's here?" Regina asked. "On another planet five billion years in the future?"

"It's in that city across the harbor." The Doctor said. "Somewhere."

"I was about to use magic to find it." Clara said.

"Let me." Regina said. "Let someone who actually knows what they're doing find it. Then we can use its power to send the ship back in time."

"Why don't we just take the TARDIS?" Neal asked.

"I can take all the people, but I can't fit the Jolly Roger through the TARDIS doors." The Doctor said. "We'll need the Eye if you want your ship to go back to Storybrooke with you."

Clara went over to the Doctor and whispered in his ear.

"Why don't you just use the Eye that's in the TARDIS to do that?" She asked.

"Because, if I just send them home now, they won't help us find the Eye." The Doctor said.

"So how do we find the Eye?" Hook asked.

"I'll find it." Regina said. "Somewhere in that huge city, I'll find it."


	2. The Awakening part 1

Chapter 2: The Awakening part 1

The Doctor and Clara boarded the Jolly Roger to meet the others on board. They had a warm reunion with Tinker Bell. They recognized many of the lost boys who were going to Storybrooke to find their families. They also recognized Felix, Pan's eternally loyal lost boy. The only truly new face they saw was that of Wendy Darling.

"Doctor." Neal said. "This is Wendy. Pan kept her prisoner on Neverland for decades. Her brothers are in Storybrooke and we're bringing her back to them."

"Another English girl." Clara said. "Always a pleasure."

What no one realized was that Peter Pan was not back in Neverland at all. Pan, had used magic to change bodies with Henry. Now, he walked around the ship in Henry's body. Regina remained on the land while she cast her magic spell to locate the Eye of Birth. The other heroes also returned to the ship to converse and plan for what would happen once they got into the city.

"Henry and the lost boys are staying here." Mr. Gold said.

"I agree." Emma said. "Then the rest of us can go looking for the Eye."

"We can't just leave them all unsupervised." Mary Margaret said.

"Yes we can." Gold said. The Dark One then waved his arm. Suddenly, every lost boy closed his eyes and fell to the ground. They had all been magically put to sleep. Henry had fallen asleep as well. "They'll stay asleep until I use magic to wake them up."

Regina suddenly used magic to transport herself onto the ship.

"What happened ?" Regina asked.

"I put the boys to sleep so they won't cause any trouble while we're away." Gold said.

"Where is the Eye?" The Doctor said.

"I'll show you." Regina said.

The former Evil Queen then waved her arms. As she did, everyone who was awake was consumed by magic smoke and disappeared from the Jolly Roger. The Doctor, Clara, Regina, Emma, Hook, Neal, Mary Margaret, David, Gold, Tink, and Wendy were all transported to a sidewalk in the city of New New York. They were surrounded by skyscrapers that were thousands of feet tall. Flying cars zoomed through the air. There were all kinds of alien creatures on the ground moving next to them. Directly in front of the large group was a small building that looked like the Parthenon in Athens. It seemed so out of place with all these futuristic buildings. Across the top were written the words "Universal History Museum".

"It's a museum." The Doctor said. "It must contain exhibits about the history of the universe."

"The Eye is in there?" David asked.

"I'm sure it is." Regina said.

So, the time travelers and the heroes of Storybrooke walked up the steps and into the museum. It was only one large white room on the inside. It seemed to be far too small to house the history of the universe. There were some other people in the museum, but not many. There were some paintings on the walls and a welcome center with desk and a stack of maps of the museum. The Doctor grabbed one and studied the map.

"The history of the universe?" Clara asked. "This isn't even enough space for the history of England."

"There's a whole other level downstairs. The rest of the museum is underground and according to the map, it's massive." The Doctor said.

The group then followed the Doctor to the other end of the white room, where they found a small staircase leading downward that they hadn't noticed before. Everyone then descended down the stairs into the largest room they'd ever seen. The walls and floor were white, just as upstairs. However, no one could see the end of the room. The walls were decorated with pictures and statues of famous battles, emperors, aliens, and everything one could possibly imagine. There were display cases scattered about that displayed various artifacts gathered from all sorts of planets and time periods.

"Finding the Eye will be even harder than we thought." Hook said.

"It's in the dangerous articles section." The Doctor said as he studied the map. "Follow me."

They group spent the next fifteen minutes walking through what felt like a maze of alien history. They noted pictures of Sontarans and statues of Time Lords. There was a whole section on the Time War. Eventually, they came to the dangerous articles section. Everything here was not deemed dangerous now, but rather at one point it was dangerous. I was mostly contained old alien laser guns. In the center of the room was a small display case. Inside this case was a small green glass eyeball. Through the clear glass, the Doctor could tell that this was the Eye of Birth. The Doctor read about it on a small plaque next to the case. The Eye was found outside the city and was brought to the museum as a historical artifact. The legend of the Eye was well known and the museum hoped to attract visitors by putting it on display, but that didn't really happen. Next to the display case were four dead Daleks. They were merely lifeless Dalek shells used for display purposes. On the other side, were four lifeless Cyberman shells. Two of the most feared beings in the universe had been reduced to museum exhibits five billion years in the future.

"Let's take it and go." Regina said.

"Are you stupid?" The Doctor asked her. "There will be alarms and police if we just go about and take it. This isn't ordinary glass. It's pressurized. If you touch it, alarms will sound."

Regina became angry that the Doctor called her stupid. She tried to contain her anger, but she was so determined to get back home that she had a hard time with it. Her magic became slightly unstable. Then, the glass containing the Eye began to crack. Regina had accidentally used magic and it cracked the glass. Just as the Doctor predicted, an alarm sounded throughout the museum. Police would arrive soon.

"There's no point in being gentle now." Regina said.

Regina then reached out her hand. Then, the glass shattered completely and the green Eye flew into her hand. However, Regina's magic was still slightly unstable. This caused the Eye to glow. As it did, the four Dalek bodies and the four Cyberman bodies began to glow as well.

"Regina!" Emma shouted. "What are you doing?"

"Nothing!" Regina yelled back.

Suddenly, the eyestalks on the Daleks started to glow bright blue and the Cybermen started to move. Regina had inadvertently used the Eye's power to revive two deadly species of alien killers.

"Delete." The Cybermen said.

"Exterminate." The Daleks cried.


	3. The Awakening part 2

Chapter 3: The Awakening part 2

The Doctor, Clara, Regina, Emma, Mary Margaret, David, Hook, Mr. Gold, Neal, Wendy, and Tinker Bell stood deep inside the Universal History Museum in New New York. They found the Eye of Birth, but Regina accidentally used it to awaken four Daleks and four Cybermen, who were all ready to begin killing again. However, the museum's police force soon arrived and started firing lasers at the Daleks and Cybermen, to no avail. The aliens' attention was drawn from the Doctor and the Storybrooke heroes to the police.

"Delete." The Cybermen all said in unison.

"Exterminate!" The Daleks all yelled.

Soon the Daleks and Cybermen began firing at the police, effectively killing them. Then, they pushed forward into the rest of the museum to continue their killing spree, leaving all the fairy tale characters behind and unharmed.

"Great job Regina." Tink said. "You unleashed the Daleks."

"It was an accident." Regina said in an angry tone.

"Who were those metal men?" Wendy asked.

"Cybermen." The Doctor, Mr. Gold, Neal, and Clara all said at the same time.

"How do you two know about the Cybermen?" The Doctor asked.

"A witch." Mr. Gold said. "The one I warned you about when we came back from Oz. She used Cybermen to terrorize me and my son back in the Enchanted Forest."

"This has nothing to do with her." Neal said. "These Cybermen appear to be acting on their own."

"I used the Eye to wake them up, I'll use the Eye to destroy them." Regina said.

"We'll have to catch them first." The Doctor said. "There are over ten million people in this city and they are all at risk until we destroy the Daleks and the Cybermen."

"Let's catch them before they leave the museum." Clara said.

Heading Clara's advice, the group ran after the Cybermen and Daleks, who were moving through the large underground museum quite quickly. The team ran through broken paintings and alien bodies that the aliens left behind on the ground. However, the group was never able to catch up to the Daleks or the Cybermen. They eventually came to the stairs that led to the above ground level. Once all of them made it back upstairs, they saw that the Daleks and Cybermen had completely destroyed the museum. They then ran out the doors and onto the sidewalk. Th street was deserted. All the people and aliens had clearly seen the Daleks and Cybermen and fled. They looked down the right side of the street and saw the four Cybermen in the distance as they moved farther away. Down the left side of the street, the four Daleks were also far away and getting farther. The Daleks and Cybermen had gone their separate ways.

"What do we do now?" Emma said.

"Same plan." The Doctor said. "We destroy them before they do any more damage.

"We'll have to split up." David said.

"We just put our family back together." Mary Margaret said.

"We need to split up and take them both on at the same time." Hook said. "If we focus all our energy on either the Daleks or the Cybermen, the other will kill more and grow stronger."

"We only have one magical Eye." Regina said. "It should be used on the Daleks first. They're far more dangerous."

"Regina will lead a group to find and destroy the Daleks." The Doctor said. "Joining her will be me, Snow, Emma, Neal, and Wendy. The rest of you will go after the Cybermen. If you don't like your group, too bad. We don't have time to bicker about it. We need to move."

Then, just as the Doctor said, the group split up. Clara, David, Mr. Gold, Hook, and Tink ran after the Cybermen, while the others engaged in a hunt for the Daleks.


	4. The Cyber Army

Chapter 4: The Cyber Army

Clara, David, Mr. Gold, Hook, and Tink ran down the street after the Cybermen. It seemed that since Regina had the magic Eye, they would have to rely on Clara and Mr. Gold's magic to destroy them. There were only four of them, but the Cybermen would still not be easy to defeat.

"So," Clara said, trying to make some conversation as they ran, "what's been happening in Storybrooke, aside from Peter Pan kidnapping Henry?"

"There might not be a Storybrooke anymore." Mr. Gold said. "After Greg and Tamara left with Henry, I gave Belle a spell that would shield the town so that Pan couldn't send anymore of his henchmen in. If she somehow failed to cast it in time, we may be returning to an entirely different Storybrooke."

"Try not to think about that now." Hook said. "We're trying to destroy metal aliens."

"How do you know the Cybermen?" Tink asked Clara.

"The Doctor took me and some kids I was looking after to a planet that used to be an amusement park." Clara said. "An entire army of Cybermen invaded the planet and the Doctor in a manner of speaking, but that was awhile ago back when he had the younger face."

Suddenly, something strange happened. The five of them stopped running and looked around. All around them was destruction from the Cybermen. They had partially destroyed buildings, cars, and the road. The street was littered with debris and some small fires. However, it was absolutely silent. There were no people or aliens to be seen or heard. It was as if this section of the city had become a ghost town.

"The Doctor said there were ten million people in this city." David said. "Why are none of them here?"

"They were all killed by the Cybermen." Tink said.

"Then shouldn't we be seeing dead bodies?" Clara asked. "The people aren't dead or hiding. They've been taken."

"What for?" Hook asked.

"Something terrible." Gold said. "A fate worse than death in many ways."

To the left of them was a set of stairs that led down into the ground. This was clearly an entrance to an underground subway station. The group heard vague noises coming from the darkness down there.

"What's down there?" David asked.

"I fear it may already be too late." Gold said.

"What are you talking about?" Hook asked.

Mr. Gold then conjured a magic fireball on his palm and descended into the darkness of the staircase. The others followed him. The fire on his arm served as a light. Apparently the Cybermen had come down here and turned out the lights. Eventually, they came to the bottom. From what Clara could see, she thought it looked no different than any other subway station in London or New York. However, Clara could not see everything. No one could. They could only see as far as the light from the Dark One's fire would extend. They moved further into the station very cautiously. Soon, a Cyberman stepped into the light and addressed the group.

"You are compatible." The Cyberman said.

"Compatible?" David asked. "For what?"

Mr. Gold, then raised his arm high into the air. Then, they fireball shot up to the ceiling. Once it hit the ceiling, the ball of fire expanded so that more light could be seen across the entire station. Now that they could see what was around them, the group saw that they were surrounded by hundreds of Cybermen. This seemed impossible. Regina had only woken four Cybermen.

"Where did they all come from?" Tink asked.

"They're the people." Clara said. "They've been converted."

"Into Cybermen?" Hook asked.

"Yes." The Dark One replied.

"You will be converted or you will be deleted." The Cyberman said.

Mr. Gold then waved his arm, consuming himself, Clara, Hook, Tink, and David in magic smoke and transporting them back to the outside street.

"We can't take on that many of them ourselves." Clara said.

"We need the Eye. It's the only thing here with enough power to stop all those Cybermen." Gold said.

"Regina has it." David said. "She needs it for the Daleks."

"The Daleks will only kill people, but the Cybermen will continue to grow in number the longer we wait." Gold said.

"We need to warn them before it's too late." Clara said.


	5. Magic vs The Daleks

Chapter 5: Magic vs The Daleks

The Doctor, Regina, Mary Margaret, Emma, Neal, and Wendy ran down the chaotic streets of downtown New New York. They were in pursuit for the four Daleks that were rampaging through the city and killing all forms of life as they went along. Regina was holding the Eye of Birth, a magical object with enough power to easily destroy the Daleks. Emma had also been practicing her magic in Neverland and could now help Regina if she needed it.

"So how do you all know the Daleks?" Emma asked as they kept running. "I've never heard of them in any fairy tales."

"Peter Pan once used powerful magic to control an entire army of Daleks and send them to every corner of the universe looking for the boy with the heart of the truest believer." Regina said.

"That was back when I was pregnant with you." Mary Margaret said to Emma.

"The Daleks are killers." Neal said. "Pan was obsessed. The entire time I was a lost boy, he would always talk about them."

"He used to threaten me." Wendy said. "He said that once he got a hold of the Daleks, he wouldn't need me anymore and he'd have them kill me."

"Where do they come from?" Emma asked.

"A long time ago on another planet." The Doctor said. "They were created by a madman."

"Can they be destroyed?" Emma asked.

"Yes." The Doctor said. "But it's not easy."

"It's easy with magic." Regina said.

They soon found a spot in the road where a flying bus had crashed into the ground. It had been shot down by the Daleks. The four Daleks then surrounded the bus as the terrified people and aliens inside it watched helplessly.

"Hey!" The Doctor shouted.

Immediately, the Daleks turned their attention to the Doctor and the Storybrooke heroes. They scanned him and knew that he was a Time Lord. They abandoned the bus entirely and moved now to kill the Doctor and his friends.

"Exterminate!" The four Daleks cried.

"Regina." Emma said. "Now would be a good time to do something."

The green Eye started to glow in Regina's palm. Then, the former Evil Queen raised it up to her lips and whispered into it. Then, the four Daleks became consumed by a green light and then violently exploded in the air. Regina had successfully used magic to defeat the Daleks. Suddenly, a purple cloud of smoke appeared, revealing Mr. Gold, Clara, Hook, David, and Tink.

"We just destroyed the Daleks." Neal said. "What about the Cybermen?"

"That's what we came to warn you about." Tink said. "There aren't just four Cybermen anymore."

"What do you mean?" Wendy asked. "How can there be more?"

"They started converting the people on this world into Cybermen." David said.

"How did they do that?" Mary Margaret asked.

"Painfully." Mr. Gold replied.

"How many Cybermen are there now?" The Doctor asked.

"Hundreds." Hook said. "We need the Eye to destroy them."

Suddenly, the group heard the sound of marching in the distance. It was the distinct sound of feet stomping on the ground. As they turned and looked behind them, they saw a small army of Cybermen steadily making its way towards them.


	6. Victory of the Master part 1

Chapter 6: Victory of the Master part 1

The Doctor, Clara, Emma, Regina, Neal, Mr. Gold, Hook, Tink, Mary Margaret, David, and Wendy stood on the city street in downtown New New York and watched a massive army of hundreds of Cybermen march towards them. Regina seemed to be standing still in shock, but she was holding the Eye of Birth, an object that easily had enough power to destroy the Cyber Army. However, it seemed Regina was too stunned to do anything. So, Mr. Gold snatched it out of her hand it took it for himself.

"What are you doing?" Regina asked. "Give it back!"

"You weren't doing anything." Gold said. "Someone has to use this eye to stop them and they have to do it now."

Suddenly, the Eye began to glow. Gold was about to raise it to his lips and whisper a command into it that would eradicate the Cyber Army. However, before he could do anything, he was consumed by a cloud of magic smoke and disappeared. Everyone else was shocked. The only thing that could save them and the city from the Cybermen was the Eye, but for an unknown reason, the Dark One disappeared with it.

"I knew we couldn't trust him." Neal said.

"Doctor." Clara said. "What do we do now?"

"Magic." The Doctor said. "Use your magic to hold them off for now until I think of something."

At his request, Regina, Emma, and Clara stepped in front of the group as the Cyber Army kept becoming less and less distant. The three magical women raised their arms in the air and soon created a large magic purple bubble that surrounded the group and acted as a defensive shield. Then the Cybermen became close enough to attack. They soon started firing hundreds of laser blasts at them. They blasts hit the shield, but we're not strong enough to break it. However, with each blast, the shield became weaker and weaker. With hundreds of lasers hitting the shield at once, it would certainly not last long. The Doctor would have to think of something quick.

* * *

Mr. Gold appeared in front of the TARDIS in a field just outside the city.

"How did I get here?" Mr. Gold asked out loud.

"I summoned you." A familiar voice called from behind him. Mr. Gold turned around slowly and dreaded the very sight before him. He saw his most hated enemy, Missy the Time Lady, holding the Dark One Dagger. "Did you miss me?"

"I'd hoped you'd be dead by now." Gold said.

"I've been alive longer than you old friend." Missy said.

"How did you get the dagger?" Gold asked.

"When you went down into that dark subway station and discovered the Cyber Army." Missy said. "I was there hiding. I snatched it from your pocket when you were all shocked and afraid of the Cybermen. You didn't even notice."

"Why didn't the Cybermen kill you?" Gold asked. "These aren't your Cybermen. They were reanimated in a museum."

"True, but I know how the Cybermen work." Missy said. "I teleported in and teleported out unnoticed and now I have your dagger."

"Is this the day you were talking about all those years ago?" Gold asked. "You said I would belong to you."

"Oh you will." Missy said. "But no. Today is not the day. I am going to give the dagger back to you, but you have to make me a deal first. I know how you love those."

"What kind of deal?" Gold asked.

"A magic deal." Missy said. "I know you know what I'm talking about. A deal bound by magic can never be broken. Even if you try to resist, magic will force you to carry out the deal."

"What deal do you want to make?" Gold asked.

"I'll give you the dagger if you give me the Eye of Birth." Missy said. " And when my victory day does come, you will be by my side."

"Never." Gold said.

"Think about what happens you don't." Missy said. "Since I have the dagger, I get control of you anyway. I'll order you to come back home with me. Then I'll have the Eye, the Dagger, and you. Without the Eye, your son will be killed by the Cybermen. I'm offering you the deal because it's much more exciting and fun. I don't want you to hate me. I'm trying to be polite and give you a choice."

"If I give you the Eye, you won't use it to save Bae." Gold said. "He dies either way."

"I'll make that part of our magically binding deal." Missy said. "The first thing I'll, do once I get the Eye is destroy the Cybermen and save your son."

"Fine." Gold said with a passive aggressive tone. "Only because there's no other way to save my son."

Missy and the Dark One then shook hands. As they did, their palms started to glow. Then, they let go and the light faded away. It was done. They were now bound by magic to obey the terms of the deal. Missy returned the Dark One Dagger to Mr. Gold and he forfeited the Eye to Missy. At long last Missy had finally achieved her goal. She was holding one of the most powerful magic objects in existence and she would use it to achieve her ultimate grand plans in the future. However, the Cybermen were still tearing apart New New York and were about to kill the Doctor, Clara, Baelfire, and everyone else in the city.


	7. Victory of the Master part 2

Chapter 7: Victory of the Master part 2

She did it. Missy had finally done it. She got one of the three Eyes of the Mystic Fates. With this, she could finally go through with her grand plans and the Dark One would be by her side.

"I've been waiting a long time for this moment." Missy said.

"Hurry up and get rid of the Cybermen." Mr. Gold said. "The deal was magically binding. You have to."

"Yes I know." Missy said. "I'm the one who brought it up in the first place."

The Cybermen continued to attack New New York. Missy and Mr. Gold could see the destruction they were doing from the field outside the city they were standing in. The Doctor, Clara, and all the heroes of Storybrooke (including Neal) were trapped in the city and were about to be killed. So, in accordance with their deal, Missy was magically bound to use the Eye of Birth to save them. The green glass eye that was the size of a baseball began to glow in her hand. Then, she lifted it up to her mouth and whispered into it.

* * *

Regina, Emma, and Clara couldn't hold up the magical shield that was protecting their group from the Cybermen much longer. The Cybermen were just too strong. Just as the shield was about to break, a miracle happened. Suddenly, every single Cyberman in New New York became consumed by a bright green light and then disappeared. They all just vanished out of thin air. The Storybrooke heroes didn't know how, but they knew the Dark One had something to do with this.

* * *

"Your son is safe." Missy said. "You'll be seeing me again very soon dear Rumple."

"When?" Gold asked. "When is this victory day going to happen? You've been alluding to it for hundreds of years."

"It won't be very long after the death of your son." Missy said before teleporting away, leaving Mr. Gold with that ominous and terrible message.

* * *

Mr. Gold appeared in a cloud of magic smoke in downtown New New York to rejoin the group.

"What happened?" Emma asked.

"What did you do?" Neal asked.

"Where is the Eye?" Regina asked, noting that he was not carrying it.

"I used the Eye to send the Cybermen away." Gold said. "But as you know, all magic comes with a price."

"What was the price this time?" Tink asked.

"The Eye is gone." Mr. Gold said. "It's lost in time again."

The Dark One was lying. He couldn't tell them of the deal he made with that conniving witch Missy. Not now while they were all starting to slowly trust him again. The Doctor was quite mad that he now had to go on another hunt across time and space for the third Eye.

"Then how are we supposed to get home?" Mary Margaret asked. "We need the Eye of Birth's power to send the ship back to Storybrooke."

"Not exactly." The Doctor said. "There are three Eyes of the Mystic Fates. The Eye of Life is in Regina's vault. The Eye of Birth has just been lost, but the Eye of Death is in the TARDIS and has been the whole time."

"You could've sent us home at any time?" Hook asked.

"Then why did we just almost die looking for the third one!" Regina yelled.

"I needed your help to find it." The Doctor said. "I figured you'd only do it if you thought it was your only way to get home."

"That's the closest you'll get to an apology from him." Clara said.

"Let's just go." Wendy said. "I'm eager to see my brothers in Storybrooke."

* * *

The Storybrooke heroes all returned to the Jolly Roger, which was anchored on the other side of the harbor next to the field. The Doctor quickly rushed inside the TARDIS to get the Eye of Death, a brown glass Eye that Clara originally stole from Peter Pan back in Neverland. Clara then used her magic to control the power of the Eye. It started to glow in her hands and she whispered into it. Then, the Jolly Roger and everyone on it was consumed by a bright light before disappearing from the water.

"They're in Storybrooke in the past where they belong." Clara said.

"I don't trust Rumplestiltskin." The Doctor said.

"Did you ever trust him?" Clara asked. "I certainly didn't. He's tried to kill me on several occasions and he still hasn't apologized."

"He knows where the Eye of Birth is, but he won't say." The Doctor said.

"Is he keeping it for himself?" Clara asked.

"I don't think so." The Doctor said. "If he was, then he would want people to know that he has all that power."

The Doctor and Clara continued to speculate on the whereabouts of the third Eye while they walked back to the TARDIS. Then, the big blue box faded away from New New York City on the planet New Earth.

* * *

Missy sat in her office at the 3W Institute. Now that she had finally acquired one of the three Eyes, she could go through with her devious plans and she could count on the Dark One to support her. She gave an evil smirk as she looked at the Eye. It was finally almost time to reveal herself to the Doctor.

* * *

 _To be continued in "Once Upon a Time Machine 2-10: The Walking Dead", the final story in season 2. It will be a grand finale as Missy and the Dark One unleash a terrible plot on all the fairy tale characters and the Doctor. Can they save the universe once again? Thanks for reading. I hope you enjoyed! Please review and let me know what you think!_


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